Sterecon was used to segment a 3D volume created by the particle averaging technique. The volume was a difference map of ribosome reconstructions with and without an antibody to protein L9. The difference map showed the antibody, but also artifacts due to stain inconsistencies. These artifacts interfered with thresholding and surface rendering of the antibody. Contours were traced around the portion of interest on each slice of the volume, using stereoscopic viewing to aid in connectivity decisions. A binary mask was then created to segment the volume and permit further visualization work. The purpose of the study was to map the epitope of protein L9 on the surface of the 50S ribosomal subunit. Protein L9 (MW 15,531) is a primary RNA-binding protein which binds to the 12S fragment of 23S RNA, containing the sites associated with peptidyl transferase activity. Protein L9 has also been cross linked to several other proteins at the peptidyltransferase center. The binding of L9 to 23S RNA contains residues implicated in the ribosomal E site and the EF-G binding site.